how to manage customer account hierarchy when deleting customers

We have imported a full hierarchy of accounts and now have identified some that need to be deleted. I know that these must be marked as obsolete , however when I do this, a warning is displayed - "customer used in business partner hierarchy". Is this something to be concerned about ? How can I remove the relationship in the account hierarchy as the accounts cannot be modified in C4C Fiori / HTML5 due to security settings?